Polypeptides having modulatory effects on cells

ABSTRACT

The present invention relates to peptides and polypeptides having the sequence SAVTFAVCAL or variants thereof, capable of binding to Calcineurin and/or to NS5A-TP2 and to their use in therapy, as well as to nucleic acid sequences and vectors encoding these peptides and polypeptides, and to cells comprising said polypeptides, nucleic acid sequences or vectors. The invention further relates to the use of the peptides, polypeptides or their derivatives to bring about phenotypic changes in mammalian cells, particularly to up-regulate calcineurin activity. The invention finally relates to a method for intracellular identification of substances which bind to calcineurin and which modulate the physiological effects of calcineurin.

The present invention relates to peptides and polypeptides havingmodulatory effects on cell functions and being capable of binding toCalcineurin and/or to NS5A-TP2. The invention also relates to nucleicacid sequences and vectors encoding these peptides and polypeptides, andto cells comprising said polypeptides, nucleic acid sequences or vectorsof the invention, as well as to the use of these peptides, polypeptides,nucleic acid sequences, vectors and cells in therapy. The presentinvention also relates to a method for modulating calcineurin activity,and to a method for intracellular identification of substances whichbind to calcineurin and which modulate the physiological effects ofcalcineurin, that is which modulate calcineurin dependent cellularpathways. The invention further relates to a method for modulatingNS5A-TP2 activity, and to a method for intracellular identification ofsubstances which bind to NS5A-TP2 and which modulate the physiologicaleffects of NS5A-TP2, that is which modulate NS5A-TP2 dependent cellularpathways.

In absence of classical genetics, the deciphering of mammalianregulatory networks rests mostly on the reverse genetics methodology,and particularly on the use of transdominant negative agents such asdominant negative alleles (1), antibodies (2), nucleic acid aptamers(3), peptide aptamers (4), antisense or small interfering RNA (5), andsmall molecule inhibitors when available (6). In most applications,these agents are designed or selected to specifically target a proteinand they are then introduced into cellular or animal models to assessthe phenotypic consequences of the targeted perturbation they exert.Another approach consists of constructing large libraries oftransdominant agents in retroviral vectors and performing geneticselections or screening to isolate library members that confer givenphenotypes. Libraries of antisense cDNAs (7), random fragments of cDNAs(8), ribozymes (9), combinatorial peptides (10), shRNAs (11) have beenused successfully to interrogate proteomes and identify new members ofmammalian regulatory pathways.

Elaborate experimental schemes have thus been developed and usedsuccessfully to identify cytostatic random cDNA fragments (12) andrandom linear peptides terminally fused to GFP (13). In both cases, acounterselection against dividing cells has been devised and, in thelatter case, coupled to a positive screening for cells that do notdivide and thus maintain a fluorescent vital dye. Whereas differentantiproliferative linear peptides have been isolated, their mechanism ofaction has not been elucidated so far (13).

Peptide aptamers are man-made combinatorial protein reagents that bindtarget proteins and can interfere with their function in living cellsand organisms (14) (4). They consist of conformationally-constrainedrandom sequence peptide loops (called ‘variable regions’) displayed by ascaffold protein. They bind their cognate targets with a strong affinityand, usually, a high specificity, which allows them to discriminatebetween closely related members within a protein family (14), or evenbetween different allelic variants of a given protein (15). So far,peptide aptamers have been mostly selected through yeast two-hybridscreening experiments, for their ability to bind a given target protein.In fewer instances, peptide aptamers have been selected for theirability to confer selectable phenotypes to yeast (16,17) and bacteria(18). Peptide aptamers selected in yeast have been used successfully toidentify their cognate target proteins by two-hybrid screening.

A number of arguments strongly support the choice of peptide aptamers toperform various phenotypic screening or selections, with the goal ofinterrogating proteomes to identify target proteins involved in theunderlying regulatory networks. First, proof of concept has beenobtained in yeast where peptide aptamers were selected for their abilityto overcome the cell cycle arrest induced by a mating pheromone, andwhere target proteins were identified by yeast two-hybrid screening(16,17). Second, peptide aptamers can target many different kinds ofintracellular proteins such as kinases, phosphatases, receptors, adaptorproteins, transcription factors, chaperones, etc., involved in manyregulatory pathways (reviewed in (4)). Third, peptide aptamers have beenshown to decorate their target proteins by binding to many differentsurfaces, involved in different functions (27). For this reason, peptideaptamers can induce a wider range of perturbations on protein functionthan other reverse genetics methods, such as gene knockout or the use oftransdominant negative alleles. Last, the double constraint imposed onthe variable regions reduces the conformational freedom and yieldstypically high binding affinities for the target proteins, therebyfacilitating their identification by different methods.

The work of the inventors illustrates the particularities of usingcombinatorial protein molecules for phenotypic screening oftransdominant reagents, as opposed to using nucleic acid molecules. Forexample, when using nucleic acid molecules (cDNA fragments, antisense,shRNAs), the identity of the target proteins is immediately unveiled bysequencing the isolated library members. In contrast, selectedcombinatorial protein molecules must be used as probes to determine theidentity of their targets, by performing yeast two-hybrid cDNA screening(10,16,17) or affinity capture experiments followed by mass spectrometry(28).

However, combinatorial protein molecules, and particularly peptideaptamers, present a considerable advantage over nucleic acid molecules.Whereas the latter can only inhibit the function of their targetproteins (by a dominant negative effect or by reducing expressionlevels), the former can cause more diverse perturbations on the functionof their targets, including an activation as observed in the presentinvention. Therefore, the use of combinatorial protein molecules forphenotypic screening or selections allows a more extensive probing ofproteomes, thus enhancing the chances to identify different targetproteins whose perturbations cause a given phenotype. Anothersignificant advantage of using peptide aptamers lies in theirapplication for drug discovery. Once their target proteins areidentified, peptide aptamers can guide the identification of smallmolecule mimicks that bind the same molecular surfaces on the targetsand induce the same biological effects (27). The use of retrovirallibraries of peptide aptamers for phenotypic screening or selectionsthus aids the unraveling of molecular regulatory networks that controlmajor biological processes and impacts positively on therapeuticresearch by facilitating the discovery of new targets and small moleculedrugs.

In the context of the present invention, the inventors have built andused a lentiviral peptide aptamer library to isolate aptamers thatinhibit cell proliferation in vitro. They have determined the identityof the target proteins of one of the isolated peptide aptamers (referredto as R5G42 (SEQ ID 22)) by performing yeast two-hybrid screeningexperiments (see table 2), and have retained NS5A-TP2 (which contains aconserved HD domain, found in many phosphatases) and CNA (the catalyticsubunit of calcineurin), as two strong target candidates. With respectto the first of these targets, no biological information is currentlyavailable for NS5A-TP2 (SEQ ID 15), except that its coding gene istransactivated by the non-structural NS5A protein from hepatitis C virus(22). The use of the R5G42 peptide aptamer could help elucidate thefunction of this protein, which could play a role in the control of cellproliferation.

With respect to the second target, calcineurin (also referred to asprotein phosphatase 3 (PPP3) or protein phosphatase 2B (PP2B)) is awell-studied protein phosphatase that plays a key role in coupling Ca²⁺signaling to cellular responses (reviewed in (23)). Calcineurin is aserine/threonine protein phosphatase constituted of a catalytic subunit,Calcineurin A (CNA) and a Ca²⁺ regulatory unit, Calcineurin B (CNB).

CNA comprises a catalytic domain at its N terminal and a regulatorydomain at its C terminal which contains the CNB binding domain, aCalmodulin (CaM) binding domain and an Auto-Inhibitory domain (AI) whichmasks the active site of CNA (see FIG. 3 b). Binding of Ca²⁺ activatedcalmodulin to CNA displaces the auto-inhibitory domain and activatescalcineurin phosphatase activity through the relief of auto-inhibition.Three isoforms of human CNA, referred to as CNA alpha (SEQ ID 16), CNAbeta (SEQ ID 17) and CNA gamma (SEQ ID 18), have been identified (seeFIG. 5). These three isoforms show from 83 to 89% identity over 90% oftheir sequence not including the N- and C-terminal tails.

Calcineurin is believed to be involved in many physiological pathwayssuch as T-cell activation, cell apoptosis, skeletal myocytedifferentiation, osteoclast differentiation and cardiac hypertrophy. InT-cells, it has been shown that activated CNA dephosphorylates the NFAT(nuclear factor of activated T cell) transcription factor, allowing itto enter the nucleus and activate the transcription of interleukin 2(IL-2). NFAT is a general name applied to a family of transcriptionfactors which consists of five members, four of which (NFATc1-NFATc4)have been shown to be regulated by Ca²⁺ and Calcineurin. Uponstimulation, NFAT proteins are dephosphorylated by calcineurin, whichallows them to translocate to the nucleus and become transcriptionallyactive (reviewed in (29). NFAT members are involved in the activation orrepression of many genes involved in diverse physiological pathways suchas T cell activation, the development of cardiac muscle, skeletal musclecells differentiation, skeletal muscle hypertrophy and the developmentof nervous systems.

The demonstration that calcineurin was the target of theimmunosuppressants cyclosporin A and FK506 has sparked a considerableinterest in this protein and has greatly facilitated the elucidation ofits function, especially in T cell activation. However, the structuralmechanisms of the activation and the inhibition of calcineurin by,respectively, calmodulin and immunophilin-immunosuppressant complexesremain poorly understood (26).

Despite numerous studies, the role of calcineurin in cell proliferationremains less clear. Cyclosporin A has been shown to inhibit theproliferation of various cells, but at concentrations exceeding thatrequired to observe an inhibition of T cell activation. FK506, althougha more potent immunosuppressant than cyclosporin A, shows a weakerantiproliferative activity (reviewed in (24)). These observationssuggest that the antiproliferative activity of these immunophilins maybe caused by the modulation of other target protein(s). Moreover,contrary to the hypothesis that calcineurin positively regulates cellproliferation, calcineurin has been shown to induce apoptosis throughdifferent mechanisms including the dephosphorylation of Bad, apro-apoptotic Bcl-2 family member (25).

In the context of the present invention, the inventors have identified anew CNA ligand that activates CNA phosphatase activity through apotentially original mechanism, since its binding site is locatedbetween the CaM-binding domain and the auto-inhibitory domain, but doesnot appear to be circumscribed to the CaM-binding domain. In accordancewith the invention, the new ligand comprises a peptide having thesequence SAVTFAVCAL (SEQ ID 20), or derivatives thereof. The inventionthus relates to this peptide, and to larger peptides or polypeptidescontaining the SAVTFAVCAL sequence, especially to peptide aptamers whichcontain the SAVTFAVCAL sequence as a conformationally-constrained loopin a protein platform. The invention further relates to the use of thepeptide or its derivatives to bring about phenotypic change ineukaryotic cells, in particular in mammalian cells, particularly toup-regulate calcineurin activity.

This application describes the first phenotypic selection of peptideaptamers in mammalian cells. It also describes the first identificationof a functional perturbation of a protein targeted by combinatorialprotein molecules isolated from an antiproliferative screening.

More specifically, the invention relates to a polypeptide comprising orconsisting of

-   -   (i) the amino acid sequence SAVTFAVCAL (SEQ ID 20), or    -   (ii) the amino acid sequence GPSAVTFAVCALGP (SEQ ID 21), or    -   (iii) a variant of the amino acid sequence (i) or (ii) having        one amino acid change.

According to the invention the term polypeptide signifies an amino acidsequence of 9 or more amino acids. Polypeptides consisting exclusivelyof amino acid sequences (i), (ii) or (iii) as defined above are alsoreferred to herein as peptides of the invention.

The polypeptides of the invention are capable of binding tointracellular molecular targets in eukaryotic cells, in particular inmammalian cells. The binding of the polypeptides of the invention totheir intracellular target has a modulatory effect on the cell. Suchtargets include Calcineurin and/or NS5A-TP2. The interaction of thepolypeptide with its target gives rise to a phenotypic change in thecell for example an antiproliferative activity, an apoptic effect or adifferentiating effect on mammalian cells.

In a preferred embodiment, the polypeptides of the invention bind toproteins which comprise at least the sequence extending from amino acid378 to 500 of the beta isoform of CNA, or analogous positions in thealpha and gamma isoforms. In another preferred embodiment, thepolypeptides of the invention bind to native CNA, i.e. as occurring inmammalian cells or human cells, more particularly, free of two-hybridreporter components.

The princeps peptide of the invention is the decapeptide (i):

SAVTFAVCAL (SEQ ID 20)

According to the invention, this decapeptide may be extended at theamino and/or carboxy termini by the addition of further amino acids, forexample from one to 300 amino acids, preferably one to 80 amino acids,at either or both sides. The peptide (ii), having 14 amino acids andhaving the sequence:

GPSAVTFAVCALGP (SEQ ID 21)

is a particularly preferred embodiment of the invention in this regard.

The invention also encompasses variants of the peptides (i) and (ii)having one amino acid difference with respect to the peptide (i) or(ii), wherein ‘difference’ (or ‘change’) signifies the substitution,deletion or insertion of one amino acid in the parental sequence (i) or(ii). Said variants are referred to herein as sequence (iii).

Particularly preferred peptide variants (iii) of the invention are thosein which one amino acid in the parental sequence (i) or (ii) issubstituted by a different amino acid, for example by an amino acidsharing a same property such as polarity, acidity, basicity orhydrophobicity. In one embodiment, one amino acid in the in theC-terminal portion of the (i) or (ii) sequence is substituted by anotheramino acid. In a preferred embodiment, the substituted amino acid isneither the serine nor one of the two valine amino acids of the (i) or(ii) parental sequence. In a most preferred embodiment, thephenylalanine amino acid is substituted by an isoleucine amino acid.

According to the invention, the amino acid sequence (i), (ii) or (iii)may be part of a larger polypeptide i.e. covalently joined at its aminoand/or carboxy termini to other amino acid residues or sequencesthereof. For example, the amino acid sequence (i), (ii) or (iii) may beembedded within a larger polypeptide, or may be fused at one or bothextremities to a heterologous polypeptide, giving rise to a fusionprotein. The total length of such a chimeric polypeptide, including theamino acid sequence (i), (ii) or (iii), is normally from 14 to 600 aminoacids, for example 14 to 150 amino acids.

According to a preferred embodiment, the amino acid sequence (i), (ii)or (iii) is conformationally constrained by covalent binding to ascaffold molecule, preferably at both C and N termini, i.e. the sequence(i), (ii) or (iii) is doubly constrained. The scaffold (also called‘platform’) can be any molecule which is capable of reducing, throughcovalent bonding, the number of conformations which the sequence (i),(ii) or (iii) can assume. Examples of conformation-constrainingscaffolds include proteins and peptides, for example thioredoxin andthioredoxin-like proteins, nucleases (e.g. RNaseA), proteases (e.g.trypsin), protease inhibitors (e.g. eglin C), antibodies orstructurally-rigid fragments thereof, fluorescent proteins such as GFPor YFP, and conotoxins. A conformation-constraining protein or peptidecan be of any appropriate length, for example from 5 to 150 amino acids,preferably 5 to 40 or 5 to 60 or 80-120 amino acids. Other suitableplatform molecules include carbohydrates such as sepharose. The platformmay be a linear or circular molecule, for example, closed to form aloop. The combinatorial constraint may also be bought about by covalentbonding of the N- and C-terminal amino acids of the peptide to eachother. The amino acid sequence (i), (ii) or (iii) may e part of apeptide aptamer.

The platform is generally heterologous with respect to the amino acidsequence (i), (ii) or (iii), i.e. the platform is not of the same originas the amino acid sequence (i), (ii) or (iii).

The association of the platform and amino acid sequence (i), (ii) or(iii) generally does not exist in nature. In particular, the associationof the platform and amino acid sequence (i), (ii) or (iii) is preferablynot an aquaporin 7 molecule.

According to a preferred embodiment, the scaffold is a protein and theamino acid sequence (i), (ii) or (iii) is located between two cysteinesin the scaffold protein. In this manner, the amino acid sequence (i),(ii) or (iii) and any flanking amino acids form a conformationallyconstrained loop structure which has proven to be particularly suitableas an intracellular recognition molecule.

Human thioredoxin (hTRX) (SEQ ID 19) or E. coli thioredoxin A (TRX-A),or a thioredoxin-like molecule (TRX-like), are particularly preferred asscaffolds. In this case, the amino acid sequence (i), (ii) or (iii) islocated in the active-site loop, between the two cysteines at positions32 and 35 (see amino acid sequence of human thioredoxin illustrated inFIG. 7), or analogous positions in thioredoxin-like (TRX-like)molecules. Thioredoxin-like proteins are defined herein as proteinshaving at least 50%, preferably at least 80% and most preferably atleast 90% identity, for example 95% identity, with the amino acidsequence of human thioredoxin (SEQ ID 19) over an amino acid sequencelength of 80 amino acids (see FIG. 7). Thioredoxin-like molecules alsoinclude peptides which have a three-dimensional structure substantiallysimilar to that of human or E. coli thioredoxin, for exampleglutaredoxin. A particularly preferred thioredoxin platform is nativehuman thioredoxin (SEQ ID 19), or alternatively, human thioredoxinhaving one or more point mutations in the amino acid sequence flankingthe active site. In particular, thioredoxin molecules in which one, twoor three amino acids of the native human sequence are substituted bydifferent amino acids, are especially suitable as scaffolds of theinvention. Indeed, the inventors have demonstrated that the bindingaffinity of the polypeptide to its intracellular target can be modulatedby variation of the amino acid sequence of the human TRX (SEQ ID 19).

In a preferred embodiment, thioredoxin molecules in which one amino acidof the native hTRX sequence is substituted by a different amino acid,are used as scaffolds for the polypeptides of the invention.Particularly preferred variants of human thioredoxin are those in whichone amino acid is substituted by a different amino acid, for example byan amino acid sharing a same property such as polarity, acidity,basicity or hydrophobicity.

Alternatively, one amino acid is substituted by a different amino acidhaving a different polarity, acidity, basicity or hydrophobicity. In apreferred embodiment, the substituted amino acid is neither one of thefive amino acids on the amino-side of the cysteine at position 32, norone of the five amino acids on the carboxy-side of the cysteine atposition 35 of hTRX. In yet another preferred embodiment, thesubstituted amino acid is one of the five amino acids on the amino-sideof the cysteine at position 32, or one of the five amino acids on thecarboxy-side of the cysteine at position 35 of hTRX.

In a most preferred embodiment, the polypeptide of the invention has oneof the sequences listed in FIG. 8 (SEQ ID N^(o) 22-29, 33 or 34).

The amino acid sequences (i), (ii) or (iii), when conformationallyconstrained within a platform such as h-TRX or TRX-like proteins will bereferred to herein as peptide aptamers.

According to a preferred embodiment of the invention, the polypeptide iscapable of binding to Calcineurin and/or to NS5A-TP2. In one embodimentthe polypetides of the invention are capable of binding to CNA andNS5A-TP2. In another embodiment, they are capable of binding to CNA butnot to NS5A-TP2. In yet a further embodiment, they are capable ofbinding to NS5A-TP2 but not to CNA.

In this context, unless otherwise specified, “calcineurin” or “CNA”signifies full length Calcineurin A (human) or a polypeptide comprisingat least amino acids 378 to 500 of the beta isoform of human CNA.

“Binding” signifies non-covalent interaction between the polypeptide andCalcineurin and/or NS5A-TP2, sufficient to give rise to a detectabletranscriptional signal in a two-hybrid assay. Affinity of binding isgenerally between 10⁻⁶M and 10⁻⁹M.

Intracellular binding between the polypeptide of the invention andcalcineurin and/or NS5A-TP2 can be determined for example by perfoming atwo-hybrid (2H) assay, as described in WO 96/02561, in which thepolypeptide is the bait protein and calcineurin or NS5A-TP2 is the preyprotein. Alternatively calcineurin or NS5A-TP2 can be the bait and thepolypeptide can be the prey.

The two-hybrid assay uses the activation of a reporter gene by thebinding of a reconstituted transcription factor onto its operatorsequences, and the fact that in most eukaryotic transcription factors,the activating and binding domains are modular and can function in closeproximity to each other without direct binding. This means that evenwhen the transcription factor is split into two fragments, it can stillactivate transcription when the two fragments are indirectly connected.

In yeast two-hybrid screening, separate bait and prey plasmids aresimultaneously introduced into the mutant yeast strain. Bait plasmidsare engineered to produce a protein product in which the binding domain(BD) fragment is fused onto the bait protein. Prey plasmids areengineered to produce a protein product in which the activating domain(AD) fragment is fused onto the prey protein. After transfection of theyeast with both plasmids, interaction between the bait and the preyprotein activates the transcription of the reporter gene, and therebyallows the interaction to be detected.

Common transcription factors used for yeast two-hybrid screening includeGAL4 and the DNA-binding domain of the E. coli protein LexA.

In one embodiment, reporter genes can encode for enzymes that allowsynthesis of specific amino acids that the mutant yeast strain isotherwise unable to produce, such as for example leucine and adenine.Thus, yeast containing a bait protein and a prey protein which interact,will grow on media lacking those amino acids.

Another commonly used reporter gene is lacZ which when activated resultsin yeast colonies that generate a blue colour under certain conditions.

Extracellular or in vitro binding between the polypeptide of theinvention and calcineurin and/or NS5A-TP2 can be determined by classicalmethods analogous to those used for immunodetection, for example, byimmobilising the polypeptide on a support and contacting with labelledcalcineurin or NS5A-TP2. Alternatively calcineurin or NS5A-TP2 can beimmobilised on a support and contacted with the polypeptides of theinvention carrying a detectable label.

The polypeptides of the invention generally bind to calcineurin throughsaid amino acid sequence (i), (ii) or (iii), and preferably bind to thecalcineurin subunit A. They generally bind to at least one, andpreferably all of the alpha (SEQ ID 16), beta (SEQ ID 17) or gamma (SEQID 18) isoforms of human calcineurin A (CNA) (see FIG. 5).

The polypeptides of the invention preferably bind to CNA at a site, orat a plurality of sites, located within the sequence extending from theamino terminal of the calmodulin binding domain to the carboxy terminalof the auto-inhibitory domain of CNA (see FIG. 3 b). The site is howevernot limited to the calmodulin binding domain, as this domain is not initself sufficient for binding.

The polypeptides generally binds to the human CNA beta isoform at itsC-terminal through a site, or at a plurality of sites, located withinthe sequence extending from amino acid 378 to 500, or analogouspositions in the alpha and gamma isoforms.

The polypeptide of the invention also generally binds to NS5A-TP2 (SEQID 15) (see FIG. 6). The precise binding site of the polypeptide toNS5A-TP2 has not been determined by the inventors.

The polypeptide of the invention are capable of exerting a modulatoryeffect on a cell, for example at least one cellular function isupregulated, downregulated, activated or eliminated, for examplecalcineurin-dependent pathways or NS5A-TP2 dependent pathways. Mostpreferably, the peptides and peptide aptamers of the invention give riseto a specific detectable phenotype or change in phenotype on binding tothe target within a cell. For example, the specific detectable phenotypeconsists in the expression of a reporter gene, a modification of theproliferative rate of the cells, cell apoptosis, a modification of celldifferentiation or resistance to cell death. In a preferred embodiment,the polypeptides of the invention have a differentiating effect onosteoclasts in the absence of RANKL, i.e. the polypeptides of theinvention enhance the formation of osteoclasts in the absence of RANKL.In another preferred embodiment, the polypeptides of the inventionreduce muscular atrophy, indicating enhancement of muscledifferentiation.

Most preferably, the specific detectable phenotype brought about by thebinding of the polypeptide of the invention to its target, is anantiproliferative activity in mammalian cells, particularly in humancells.

The antiproliferative activity can for example be detected by infectingthe cells labelled with the fluorescent vital dye CMTMR which cellsincorporate and dilute as they proceed through division cycles, with alentiviral vector encoding the polypeptide of the invention inconditions in which the polypeptide is expressed in the cells. The cellswhich do not divide or divide at a slower rate maintain a higherfluorescence level which can be detected, for example by flow cytometry(see FIG. 2A).

Alternatively, antiproliferative activity can be detected bytransfecting the cells with a plasmid encoding the polypeptide of theinvention in conditions in which the polypeptide is expressed in thecells, cultivating the cells for a period during which they wouldnormally form detectable colonies, for example one to three weeks,detecting the colonies for example by staining of the cells that growwith crystal violet and counting the colonies (see FIG. 2B).

The invention also relates to a nucleic acid sequence comprising orconsisting of a sequence encoding the polypeptide of the invention asdefined above, and to a vector containing this nucleic acid sequence.Preferably, the vector is suitable for introduction and expression ofthe nucleic acid in mammalian cells, in mammalian tissue, such as muscletissue, or in a mammalian organ, for example a retroviral vector, alentiviral vector or a plasmid.

The invention also encompasses a eukaryotic cell comprising thepolypeptide of the invention as defined above, particularly a mammaliancell, or mammalian cell line, for example a murine or human cell or cellline. Particularly preferred cell types are cells of the immune system,skeletal muscle cells, bone cells or cardiac muscle cells, for example Tcells, myocytes, satellite cells, muscle fibers, osteoclasts, orosteoblasts.

The polypeptide of the invention may be introduced into the cell in anumber of different ways. For example, it can be introduced into thecell by expression of a DNA sequence encoding the polypeptide. Thismethod is generally applied when genetic manipulation of the cell or theorganism is possible. In such cases a nucleic acid molecule encoding thepolypeptide is introduced into the cell in a suitable vector, comprisingall the necessary control sequences for expression.

Alternatively, the polypeptide is introduced into the cell in purifiedform using a cell permeable agent, such as protein transduction domains(PTDs), for example penetratin.

This method is particularly advantageous for therapy when geneticmodification of the individual is undesirable. A further alternative isto microinject the polypeptide into the cell.

The invention also relates to methods for identifying substances whichmodulate the interaction between calcineurin (CNA) and a polypeptide ofthe invention. These methods allow the identification of molecules whichcan up- or down-regulate the physiological effects of calcineurin, andwhich consequently have therapeutic potential, for example the moleculesmay up-regulate the phosphatase activity of calcineurin. In particular,these methods allow the identification of molecules which can modulateNFAT-dependent activation or repression of gene transcription.

More particularly, the invention relates to a method for theidentification of substances which modulate the interaction between CNAand a polypeptide of the invention, said method comprising the steps of

-   -   (i) contacting a candidate modulatory substance with CNA and the        polypeptide of the invention in conditions in which CNA and said        polypeptide can bind, and in which said binding can be detected        by a specific signal;    -   (ii) detecting a change in the intensity of said signal; and    -   (iii) optionally recovering the candidate substance.

More specifically, this aspect of the invention includes a method forthe identification of substances which modulate the interaction betweenCNA and a polypeptide of the invention, said method comprising the stepsof

-   -   (i) introducing a candidate modulatory substance, CNA and the        polypeptide of the invention into a eukaryotic cell, in        conditions in which a specific detectable phenotype associated        to the binding of CNA with the polypeptide of the invention can        be detected;    -   (ii) detecting a change of the said specific detectable        phenotype; and    -   (iii) optionally recovering the candidate substance.

Modulatory substances or ligands identified by this method may beproteins, peptides, small organic molecules, nucleic acids, includingDNA or RNA. Small organic molecule can be defined as non polymericorganic molecules which have a molecular weight of less than 3000 Da,preferably less than 2500, 2000, 1500, 1000, 750 or 500 Da.

The interaction which is modulated by the candidate substance isgenerally the binding of the polypeptide of the invention to CNA at asite or a plurality of sites located within the sequence extending fromthe amino terminal of the calmodulin binding domain up to and includingthe carboxy terminal of the auto-inhibitory domain of CNA, particularly,the sequence extending from amino acid 378 to 500 of the beta isoform ofCNA, or equivalent positions in the alpha or gamma isoforms. The methodof the invention therefore allows identification of molecules whichcompete with the polypeptide of the invention for this binding site.Such molecules may agonise or antagonise the effect of the polypeptideof the invention, for example they may stimulate or prevent thepolypeptide of the invention from stimulating the phosphatase activityof calcineurin, and may stimulate or inhibit the anti-proliferativeeffect of calcineurin.

The method relies on the detection of a change in the phenotypic statusof the cells in the presence of the three components of the system (i.e.the candidate compound, CNA and the polypeptide of the invention),compared to the phenotypic status of the same cells when only CNA andthe polypeptide of the invention are introduced into the cells.

The specific detectable phenotype may consist of the expression of aheterologous or endogenous reporter gene, a modification of theproliferative rate of the cells, cell apoptosis, a modification of celldifferentiation or resistance to cell death.

The two hybrid assay as described in EP1582590 may be used to identifycandidate modulatory substances. In this context, the bait is usuallyCalcineurin, bound to a DNA-binding moiety, and the prey is usually thepolypeptide of the invention, bound to a gene activating moiety. Thistype of assay allows the identification of substances which modulatebinding of the polypeptide of the invention to CNA, as seen byenhancement or inhibition of reporter gene expression. The reporter genein this context is usually a heterologous reporter gene introduced intothe cells for the purpose of the assay.

If it is desired to identify substances which have the capacity tomodulate, not only the binding of the polypeptide of the invention toCNA, but also the physiological effect on the cells of this binding,then a phenotypic screen using endogenous cellular phenotypes should beused. For this type of assay, phenotypic characteristics such asexpression of an endogenous reporter gene, modification of theproliferative rate of the cells, cell apoptosis, a modification of celldifferentiation or resistance to cell death may be used as the read-outfor modulatory activity.

The invention also relates to methods for identifying substances whichmodulate the interaction between NS5A-TP2 and a polypeptides accordingof the invention.

In particular, the invention relates to a method for the identificationof substances which modulate the interaction between NS5A-TP2 and apolypeptide of the invention, said method comprising the steps of

-   -   (i) contacting a candidate modulatory substance with NS5A-TP2        and the polypeptide of the invention in conditions in which        NS5A-TP2 and said polypeptide can bind, and in which said        binding can be detected by a specific signal;    -   (ii) detecting a change in the intensity of said signal; and    -   (iii) optionally recovering the candidate substance.

More specifically, this aspect of the invention includes a method forthe identification of substances which modulate the interaction betweenNS5A-TP2 and a polypeptide of the invention, said method comprising thesteps of

-   -   (i) introducing a candidate modulatory substance, NS5A-TP2 and        the polypeptide of the invention into a eukaryotic cell, in        conditions in which a specific detectable phenotype associated        to the binding of NS5A-TP2 with the polypeptide of the invention        can be detected;    -   (ii) detecting a change of the said specific detectable        phenotype; and    -   (iii) optionally recovering the candidate substance.

Molecules which bind to calcineurin at the same site as that bound bythe polypeptides of the invention (within the sequence extending fromamino acid 378 to 500 of the beta isoform of CNA, or equivalentpositions in the alpha or gamma isoforms), may be used to modulatecalcineurin activity in vivo or in vitro. Such a method comprisescontacting calcineurin with a ligand capable of binding to calcineurinat a site located within the sequence extending from the amino terminalof the calmodulin binding domain to the carboxy terminal of theauto-inhibitory domain of CNA, in conditions suitable to allow effectivebinding between the ligand and calcineurin thereby modulating at leastone activity of calcineurin, for example phosphatase activity, and theconsequent anti-proliferative activity. According to this aspect of theinvention the ligand may be a polypeptide according to the invention,comprising or consisting of the amino acid sequences (i) (ii) or (iii),or may be a small molecule, nucleic acid or protein which binds tocalcineurin at the same site as the polypeptide of the invention.

The polypeptides of the invention can be used as therapeutic agents foruse in humans or animals, more particularly as the active ingredient inpharmaceutical compositions, optionally associated with apharmaceutically acceptable carrier. The nucleic acids encoding thepolypeptides of the invention may also be used as therapeutic agents. Aparticularly preferred embodiment is the use of a peptide (i), (ii) or(iii) of the invention in a TRX or TRX-like scaffold, particularly ahuman TRX scaffold, as a therapeutic agent. In particular, the inventionrelates to methods for treating or preventing conditions in which theup-regulation of calcineurin phosphatase activity or the activation ofNS5A-TP2 is required, by administering to an individual in need of suchtreatment, effective amounts of the polypeptide or nucleic acid of theinvention. Preferably, the administration is performed at the body siteor organ concerned by the pathology, for example muscle, bone, brain,heart, etc.

One aspect of the invention therefore relates to the use of thepolypeptide, the nucleic acid, the vector or the cell of the inventionfor the preparation of a medicament for treating or preventing adisorder which can be treated or prevented by upregulating thephosphatase activity of calcineurin or by activating NFAT in eukaryoticcells.

A further aspect of the invention relates to the use of the polypeptide,the nucleic acid, the vector or the cell of the invention for thepreparation of a medicament for treating or preventing a disorder whichcan be treated or prevented by limiting the proliferation of eukaryoticcells.

Typically, the eukaryotic cells are mammalian cells, preferably humancells, and are chosen from cancer cells, cardiomyocytes, neurones,fibroblasts, skeletal muscle cells, osteoclasts, osteoblasts or T-cells.The condition may be a pathology associated with NFAT phosphorylationstate, T-cell activation state, skeletal myocyte differentiation stage,skeletal muscle dystrophy or atrophy, neurone development or boneformation. As examples of conditions in which administration of thepolypeptide of the invention may be advantagous, reference may be madeto Osteopetrosis (or marble bone disease), Duchenne muscular dystrophy,cancer or repair of a farcted area in the heart.

In another embodiment, the invention relates to a method for enhancingtranscription of a gene in a cell, which gene is under thetranscriptional control of a regulatory element, particularly apromoter, containing at least one NFAT-response element, by introducinga polypeptide according to the invention in the cell.

A further aspect of the invention therefore to the use of thepolypeptide, the nucleic acid, the vector or the cell of the inventionfor the preparation of a medicament for treating or preventing adisorder which can be treated or prevented by the binding of thepolypeptide of the invention to NS5A-TP2 in eukaryotic cells, forexample for treating hepatitis C or a HCV induced liver tumors.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1. Design of the Peptide Aptamer Library and of theAntiproliferative Screening

(A) Schematic representation of the pBK1 peptide aptamer library. ThisSIV-derived expression system directs the expression of two cistronscoding for a EGFPf transduction marker and HA-tagged peptide aptamersconsisting of a 10 aminoacid variable region inserted within the activesite of human thioredoxin.

(B) Workflow of the screening for antiproliferative peptide aptamers.Rat XC cells are transduced with pBK1 and labelled with CMTMR. Thehighest percentile of fluorescent cells is then isolated by flowcytometry, and the peptide aptamer coding sequences are amplified by PCRfrom genomic DNA to construct sub-libraries. The sub-libraries are usedin successive iterations of this process.

FIG. 2. Antiproliferative Effect of Peptide Aptamers

(A) Progressive enrichment of peptide aptamer sublibraries inantiproliferative peptide aptamers through screening iterations. XC orHela cells were transduced with pBK1 or different R″n″ sub-librariesobtained after n screening iterations, and were labelled with CMTMR. Themean fluorescent intensity increases with the number of screeningiterations, indicating a progressive enrichment in peptide aptamersexerting an antiproliferative effect.

(B) Colony formation assays. Hela or MCF-7 cells were transfected withplasmids directing the stable expression of the Cdk inhibitor p21, alibrary of peptide aptamers from pBK1 (AptaLib), Human thioredoxin(HTRX), and peptide aptamers R7G44, R5G42, R5G52. The cells werecultured for two weeks and the colonies were stained with crystalviolet.

FIG. 3. Interaction Between Peptide Aptamer R5G42 and Calcineurin A

(A) Yeast two-hybrid mating assay. TB50α yeast were co-transformed withpSH18-34T (bearing a lacZ reporter gene) and plasmids directing theexpression of LexA alone or in fusion with peptide aptamers R5G42, R7G44or R5G52. MB210a yeast were transformed with the selected cDNA libraryplasmids directing the expression of CNAβ, CNAγ, and NS5ATP2 truncatedproteins. To obtain negative controls, MB210a yeast were alsotransformed with the empty prey plasmid (pJG4-5) and with pJG4-5directing the expression of Ras and FKBP12 prey proteins. To obtain apositive control, MB210a yeast were transformed with pJG4-5 directingthe expression of RG22 peptide aptamer prey fusion protein thatinteracts with LexA in the context of most LexA fusion proteins.

(B) Schematic representation of the CNA clones selected through theyeast two-hybrid screening and of the truncations performed on CNAβ.

CNA beta C ter-delta 1: amino acids 378 to 500

CNA beta C ter-delta 2: amino acids 378 to 456

CNA beta C ter-CaM: amino acids 378 to 423

(C) Affinity capture assay. Comparable amounts of GST-R7G44 or GST-R5G42recombinant fusion proteins were coupled to glutathione-sepharose beads.Purified calcineurin was added onto the beads and the captured moleculeswere revealed by a western blot experiment using an anti-calcineurinantibody.

FIG. 4. Stimulation of Calcineurin Activity by Peptide Aptamer R5G42

(A) In vitro calcineurin phosphatase assay. Dephosphorylation of themodel substrate pNPP by purified calcineurin was measured in presence ofvarious amounts of purified calmodulin (CaM), GST-R5G42 or GST-R7G44fusion proteins.

(B) Monitoring of BAD phosphorylation in cultured cells. Hela-Tet cellswere transfected with plasmids directing the transient expression ofBAD, CNAβ, CNB and peptide aptamers R5G42, R5G52 or R7G44. Transfectedcells were treated or not with 500 nM FK506. The expression level of BADand the phosphorylation of serine 112 and 136 residues were monitored bywestern blot experiments using specific antibodies.

FIG. 5. Human Calcineurin A Isoforms

(A) amino acid sequence of calcineurin A alpha isoform (SEQ ID 16)

(B) amino acid sequence of calcineurin A beta isoform (SEQ ID 17)

(C) amino acid sequence of calcineurin A gamma isoform (SEQ ID 18)

FIG. 6. NS5A-TP2

Amino acid sequence of NS5A-TP2 (SEQ ID 15)

FIG. 7. Human Thioredoxin

Amino acid sequence of human thioredoxin (SEQ ID 19)

FIG. 8. R5G42 and R5G42 Mutants

Amino acid sequences of R5G42 (SEQ ID 22) and of the R5G42 C2, C3, C4,C5, C7, C8, C12, N9 and N12 mutants (SEQ ID 23-29 and 33-34).

FIG. 9. Interaction Matrix Between R5G42 Mutants and CNA Beta, CNA Gammaand NS5A-TP2

The capacity of R5G42 mutants having a one amino acid change as comparedto R5G42 to bind CNA beta and gamma C-Terminal fragments (FIG. 3 b) andNS5A-TP2 was tested in yeast two-hybrid assays. CNA beta and gammaC-Terminal fragments and NS5A-TP2 were cloned in three different vectors(pSH18-34, pJK103 and pRB18-40). These three plasmids differ from eachother in the level of sensitivity of their promoter, pSH18-34 having thehighest sensitivity and pRB18-40 having the lowest. R5G42 mutants C2, C7and C8 were shown to interact with the CNA beta and gamma C-terminalfragments but not with NS5A-TP2, and R5G42 mutant N9 (SEQ ID 33) wasshown to interact with NS5A-TP2 but not with the CNA beta and gammaC-terminal fragments.

FIG. 10. Expression of Human TRX in HeLa Cells Transfected with pCI-HAor pBof Plasmids

From equivalent total protein amounts (revealed by the intensity of theanti-Actin labelling), HA labelled Trx is only detected with plasmidspCI-HA/Trx and pBof/Trx. However, in the context of pBof, the expressionlever is lower.

FIG. 11. Expression of Aptamers According to the Invention in HeLaCells.

HeLa cells were transfected with pCI-HA plasmids containing either anempty vector, Trx, R5G42, C2, C7, C8, N9 and R5G52. Expression in thecells of Trx, R5G42, C2, C7, C8 and N9 was confirmed by a Western Blot.

FIG. 12. Effect of Peptide Aptamers According to the Invention onOsteoclast Differentiation

Trx, CNA* and Peptide aptamers R5G42, C2, C7, C8 and N9 were transfectedinto RAW1 cells and left for four days in absence of the normaldifferentiation factor RANKL. CNA* is activated calcineurin A whichelicits a robust differentiation response. The results show thatdifferentiation is induced by the aptamers R5G42 and C7.

A. Transfection of RAW1 cells with an empty vector and addition of RANKLtwo days after transfection (positive control), and transfection with avector containing TRX (negative control). B. Transfection OF RAW1 cellswith vectors containing CNA* (positive control for differentiationactivation) and the peptide aptamers R5G42, C2, C7, C8 and N9

FIG. 13. Expression of Proteins in Mice Muscles After Electroporationand Denervation

Mice hind legs received an injection followed by electroporation ofplasmids containing Thioredoxin (TRX) or a control aptamer (34). Theirleft hind legs were then denerved. Control mice (CT) received only anNaCl injection. Total proteins were extracted for an analysis of theexpression of certain key proteins among which TRX, the aptamer 34 andits target (C34), Calcineurine A (CNA), beta-Tubuline (B-Tub), Bcl2 andBax. It is to be noted that the fibers having incorporated the vectors(pCI-HA-TRX, pCI-HA-34) only represent a fraction of the muscleanalysed.

FIG. 14. Specificity of Aptamers According to the Invention for CNA andNS5A-TP2

Interaction matrix between peptide aptamers R5G42, C2, C7, C8, N9, R5G44and R5G52 with CNA constructs CNA1-CNA8 (A) CNA9-11 (B) and NS5A-TP2(C). An interaction phenotype between CNA3/CNA 11, which both containthe Calmodulin binding domain (CaM) and the auto-inhibitory domain (AI)but not the CNB binding domain (CNB) and the aptamers R5G42, C2, C7, C8and N9 is observed in a two-hybrid assay. R5G44 and R5G52 aptamersrecognize neither the CNA fragments, nor NS5A-TP2. Only aptamers R5G42and N9 recognize NS5A-TP2.

CNB: CNB binding domain; CaM: Calmodulin binding domain; AI:auto-inhibitory domain

FIG. 15. Detection of the Expression of CNA Constructs in Yeast

In order to check the expression of the CNA constructs CNA1 to CNA7 inthe two-hybrid assay, a cellular lysate was performed followed byWestern Blot detection. The molecular weights of the differentconstructs are represented in the squares. For CNA5 and CNA6, no bandsare detected which is probably due to their small size (about 19 kDa)

FIG. 16. Detection of the Expression of Aptamers According to theInvention in Yeast

The lysis of the yeasts was performed on colonies obtained after themating of mat a and mat alpha strains and the determining of thetwo-hybrid phenotype. Aptamers R5G42, C2, C7, C8, N9 and R5G52 are inthe LexA-pGILDA vector. Their expression was detected unsing an antibodywhich recognize LexA.

FIG. 17. Amino Acid Sequences of CNA1-CNA11 (SEQ ID 35-45)

FIG. 18. Measure of the Tibialis Anterior Area 14 Days Post-Denervation

Vectors containing TRX, the R5G42, C7 or N9 aptamers or NaCl (control)were electroporated in mice hind legs (day 1) and an unilateralabolition of the motor innervation of the tibia muscles of the left hindleg was performed (day 3). After euthanasia of the mice (day 17) thetibialis anterior area was measured.

Without denervation, the muscle area is relatively stable from oneexperiment to another (6.532.412+/−351.070, or 5.3% of variation). Withdenervation a reduced atrophy effect of about 27% and 48% is observedwith aptamers R5G42 and N9 as compared to the atrophy effect obtainedusing the NaCl control (See FIGS. 19-20). The 100% of atrophy effect wasevaluated using the data obtained with the NaCl control.

A-B. Measure of the the tibialis anterior area with (left hind leg) orwithout (rigth hind leg) denervation—C. Section of the tibialis anteriorarea 14 days post-denervation

EXAMPLES

The inventors set out to identify and isolate combinatorial proteinreagents capable of inhibiting tumor cell proliferation.

A peptide aptamer library was built in a lentiviral expression system toisolate aptamers that inhibit cell proliferation in vitro. Using one ofthe isolated aptamers (R5G42), as a bait protein, a yeast two-hybridscreening of cDNA libraries was performed and calcineurin A (CNA) wasidentified as a target protein candidate. R5G42 binds CNA in vitro andstimulates its phosphatase activity. When expressed transiently in humancells, R5G42 induces the dephosphorylation of Bad. The use of thisligand is therefore likely to help elucidate the still elusivestructural mechanisms of activation and inhibition of calcineurin.

In the experiments reported in the following examples, the inventorshave constructed a peptide aptamer library in a simian immunodeficiencyvirus (SIV)-derived gene expression system. They have performed aniterative genetic screening to isolate peptide aptamers that inhibittumor cell proliferation. They have identified the catalytic subunit ofthe calcium-activated protein phosphatase calcineurin as a target of oneof the isolated aptamers. They have shown that this aptamer upregulatesthe phosphatase activity of calcineurin in vitro and in cultured cells.Their work has identified an antiproliferative molecule that binds andstimulates calcineurin through a seemingly original mechanism.

The inventors have shown that an antiproliferative peptide aptamer(R5G42) binds CNA and activates its phosphatase activity in vitro.Consistent with the in vitro results, the transient expression of R5G42in human cells induces the dephosphorylation of Bad on Serine 136, whichis totally reversed by FK506. The expression of R5G52, anotherantiproliferative peptide aptamer, does not affect Bad phosphorylationlevels. Altogether, these results indicate that Bad dephosphorylation isspecifically caused by the activation of CNA by R5G42, as opposed tobeing an indirect consequence of an antiproliferative activity.

The antiproliferative effect of R5G42 could stem from acalcineurin-mediated induction of apoptosis, which would only occur uponprolonged expression of the peptide aptamer.

Details of the Materials and Methods Employed in the Following Examples1 to 7 are Provided in Example 7

Example 1 Peptide Aptamer Libraries and Screening Strategy

To construct their peptide aptamer libraries, the inventors used aSIV-derived lentiviral expression vector directing the constitutiveexpression of bicistrons (transgenes and a GFP marker) under the controlof an EF1α promoter (see Example 6 for experimental procedures). Theyfirst built 12 low-complexity peptide aptamer libraries, combining twoscaffolds (human thioredoxin or a E. coli thioredoxin, whose codingsequence harbors codons optimized for expression in mammalian cells),two epitope tags (HA or 6His) and three variable region lengths (16, 10or 7 amino acids). They performed pilot experiments to determine whichlibrary yielded the highest expression level of peptide aptamers upontransduction of XC cells with viral particles. They observed that thebest combination was the HA-tagged, human thioredoxin displaying arandom peptide loop of 10 amino acids and they constructed accordinglypBK1, a high-complexity peptide aptamer library (see FIG. 1A).

To isolate library members that inhibit tumor cell proliferation, theinventors made use of the fluorescent vital dye CMTMR(5-(and-6)-(((4-chloromethyl)benzoyl)amino)tetramethylrhodamine), whichcells incorporate and dilute, as they proceed through division cycles.Those cells that do not divide maintain a high fluorescence level andcan thus be sorted by flow cytometry. Because of a significantbackground of cells that do not grow or proliferate more slowlyindependent of the expression of peptide aptamers, multiple screeningrounds were necessary to isolate peptide aptamers that exert anantiproliferative effect. The inventors thus constructed a peptideaptamer sub-library from the highest percentile of CMTMR-positive cellsobtained after each screening iteration and they submitted eachsub-library to a subsequent screening round (see FIG. 1B).

Example 2 Isolation of Antiproliferative Peptide Aptamers

The inventors used rat XC cells, derived from a RSV-induced sarcoma,which enabled them to use viral particles harboring a murine ecotropicenvelope. They performed 7 screening iterations before isolating andcharacterizing individual peptide aptamers. They determined theantiproliferative activity of the sub-libraries both in XC cells and inhuman HeLa cells. As shown in FIG. 2A, the mean fluorescence intensityof both cell lines increases gradually with the number of screeningiterations, thereby indicating a progressive enrichment ofantiproliferative peptide aptamers within the sub-libraries.

The inventors picked and sequenced 100 clones from the R5 and R7sub-libraries, obtained from the fifth and seventh screening iteration,respectively. More than 40% of the peptide aptamers isolated after theseventh screening iteration corresponded to a single library member,named R5G42. The occurrence of this aptamer was already significantafter the fifth iteration but was not detectable after the fourthiteration. Three other peptide aptamers that showed a lower occurrencewere also isolated (R7G11 (SEQ ID 30), R7G44 (SEQ ID 31) and R5G52 (SEQID 32)) (see Table 1).

The inventors wished to establish the antiproliferative activity ofthese peptide aptamers using alternative cellular models and anon-retroviral vector to express individually each aptamer. They clonedthe aptamer coding genes into a vector bearing a hygromycin selectionmarker. They also subcloned the pBK1 library into this vector, to create“AptaLib”. They continuously expressed the aptamers, the emptythioredoxin scaffold or AptaLib in Hela and MCF-7 cells for 2 weeks andthey stained the cells that grew. Aptamers R5G42 and R5G52 significantlyinhibited the proliferation of both cell lines, as compared to AptaLiband human thioredoxin. Aptamer R7G44, similarly to other aptamers (notshown), did not exert any antiproliferative effect (see FIG. 2B). Theseaptamers may originate from the remaining background of slowlyproliferating cells during the seventh screening iteration,independently of the expressed aptamers. Surprisingly, aptamer R7G11 didnot inhibit cell proliferation in this assay (not shown), despiteshowing a high occurrence in the seventh sub-library (Table 1). Thiscould be due to the fact that the CMTMR assay is more sensitive indetecting modest antiproliferative effects than the colony formationassay or that some peptide aptamers somehow enhance the CMTMR labelingof their host cells. From all these results, it was decided to focus onpeptide aptamer R5G42 and to identify its target protein.

Example 3 Identification of Calcineurin A and NS5A-TP2 as TargetProteins

The inventors performed two yeast two-hybrid screening experimentsagainst a LexA-R5G42 bait protein, using a human testis and a humanfcetal brain cDNA library. They obtained 29 and 42 reconfirmed clones,respectively. They disregarded those clones that either showed a barelydetectable two-hybrid interaction phenotype, or that cross-interactedwith control aptamers, or that corresponded to hypothetical proteins(Table 2). The inventors thus retained two candidates. The highestoccurring clone, from both libraries, corresponded to the NS5A-TP2protein, recently discovered through a systematic search for genes thatare transactivated by the non-structural NS5A protein from hepatitis Cvirus (22). No biological knowledge is currently available for thisprotein. The other remaining target candidate was calcineurin A (CNA),for which two different isoforms (beta and gamma) were selected from thetestes library (see FIG. 3A).

To confirm the interaction between R5G42 and CNA, the inventorsperformed an in vitro binding assay between recombinant purifiedGST-aptamer fusion proteins, coupled to a glutathione-sepharose matrix,and purified CNA. The GST-R5G42 solid phase readily captured CNA, asopposed to a GST-R7G44 control (see FIG. 3C).

Example 4 Mapping of the R5G42 Binding Site on CNA and Mutations ofR5G42

Mapping of the R5G42 Binding Site on CNA

The inventors set out to map the R5G42 binding site on CNA. The CNAinteracting clones selected in the yeast two-hybrid experimentscorresponded to the carboxy-terminal regions of the beta and gammaisoforms, encompassing the calmodulin-binding domain and theauto-inhibitory domain (see FIG. 3B). Among the 3 truncationsconstructed from the CNAβ selected clone (see FIG. 3B), only CNAβΔ1retained its yeast two-hybrid interaction phenotype with R5G42 (see FIG.3A and data not shown). These results indicate that the R5G42 bindingsite on CNA lies between the amino-terminus of the calmodulin-bindingdomain and the carboxy-terminus of the auto-inhibitory domain, and isnot circumscribed to the CaM binding domain. This yeast two-hybridmating assay also supports the specificity of interaction between R5G42and CNA, as R5G42 did not show an interaction phenotype with twounrelated bait proteins (RAS, FKBP12) and as R7G44 and R5G52 did notshow an interaction phenotype with CNA. R5G52, however, did not show aninteraction phenotype with peptide aptamer RG22, which interacts withLexA in the context of most (but not all) LexA fusion proteins. TheLexA-R5G52 bait protein may thus not be properly expressed and/or foldedin this yeast two-hybrid setting.

Mutations of the R5G42 Amino Sequence

The inventors explored the ability of R5G42 mutants having a one aminoacid change as compared to R5G42, to bind to CNA beta and gammaC-Terminal fragments (FIG. 3 b) and to NS5A-TP2. To this end, theyproceeded to yeast-two hybrid assays as in example 3. CNA beta and gammaC-Terminal fragments (FIG. 3 b) and NS5A-TP2 were cloned in threedifferent plasmids (pSH18-34, pJK103 and pRB18-40), which differed fromeach other in the level of sensitivity of their promoter to thebait/prey complex formation, pSH18-34 having the highest sensitivity andpRB18-40 having the lowest.

R5G42 mutants C2 (SEQ ID 23), C7 (SEQ ID 27) and C8 (SEQ ID 28) wereshown to interact with the CNA beta and gamma C-terminal fragments butnot with NS5A-TP2, and R5G42 mutant N9 (SEQ ID 33) (see FIG. 8) wasshown to interact with NS5A-TP2 but not with the CNA beta and gammaC-terminal fragments (FIG. 9). The inventors thereby showed that pointmutation in the R5G42 amino acid sequence allowed to identify mutantssequence with an increased selectivity for each of the targetsidentified for R5G42.

Binding of R5G42 and R5G42 Mutants to Subsequences of CNA and toNS5A-TP2

The inventors proceeded to further yeast two-hybrid binding assaysbetween peptide aptamers R5G42 (SEQ ID 22), C2 (SEQ ID 23), C7 (SEQ ID27), C8 (SEQ ID 28), N9 (SEQ ID 33), R5G44 and R5G52 with CNA constructsCNA1-CNA8 (FIG. 14A), CNA9-CNA11 (FIG. 14B) and NS5A-TP2 (SEQ ID 15)(FIG. 14C). The sequences of CNA1-CNA11 (SEQ ID 35-45) are shown in FIG.17. The sensitivity of this yeast two-hybrid assay was higher than inthe experiment reported above.

An interaction phenotype between each of CNA3 and CNA 11, which bothcontain the Calmodulin binding domain (CaM) and the auto-inhibitorydomain (AI) but not the CNB binding domain (CNB) and the aptamers R5G42,C2, C7, C8 and N9 was observed. R5G44 and R5G52 aptamers (negativecontrols) recognized neither the CNA fragments, nor NS5A-TP2. The onlyaptamers which recognized NS5A-TP2 were R5G42 and N9 (FIG. 14).

The fact that CNA1 and CNA2 which both contain the Calmodulin bindingdomain (CaM) and the auto-inhibitory domain (AI) as well as the CNBdomain did not interact with the aptamers of the invention appears to bedue to an artefact of the yeast two hybrid protocol. Indeed, theinventors dearly showed in the Bad dephosphorylation assay in mammaliancells commented in example 5, that endogenous CNA was activated ontransfecting R5G42 into the cells.

Example 5 Modulation of Calcineurin Activity In Vitro and In MammalianCells

Activation of CNA Phosphatase Activity In Vitro

The inventors next explored the ability of R5G42 to modulate theenzymatic activity of its target protein. To this end, they firstperformed an in vitro phosphatase assay using purified CNA andpara-nitrophenylphosphate (pNPP) as a substrate. As shown in FIG. 4A,the addition of purified calmodulin (CaM) is required to activate CNA.The addition of recombinant purified GST-R5G42 did not result in aninhibition or an exacerbation of CaM-activated CNA phosphatase activity(not shown). However, the addition of high concentrations of GST-R5G42activated CNA phosphatase activity in absence of CaM, to a levelcomparable to that observed using CaM. The addition of equal amounts ofthe control aptamer R7G44 did not produce a significant effect. Thisexperiment indicates that R5G42, like CaM, binds and activates CNAphosphatase activity in vitro.

Dephosphorylation of Bad in HeLa Cells

The inventors set out to confirm this finding in human cells. Bad is akey pro-apoptotic protein whose activity is tightly regulated by itsphosphorylation status, itself controlled by the balanced activity ofseveral protein kinases and calcineurin. Therefore, the phosphataseactivity of calcineurin in cells can be monitored by examining Badphosphorylation. HeLa cells were transfected with plasmids directing theexpression of Bad, CNAβ, CNB and either R5G42, R5G52 or R7G44. Theinventors observed that expression of R5G42 decreased thephosphorylation of Bad on serine 136, without affecting thephosphorylation on serine 112 (see FIG. 48). To demonstrate that thiseffect was caused by an upregulation of calcineurin activity, theyperformed the same experiments in presence of FK506, a well-knowninhibitor of calcineurin. The R5G42-induced dephosphorylation of Bad onserine 136 was no longer observed in presence of FK506 (see FIG. 4B).

Effect of Aptamers According to the Invention on OsteoclastDifferentiation

Osteoclasts are bone-resorbing, multinucleated cells that differentiatefrom monocyte precursors. The differentiation of osteoclasts isdependant on a tumor necrosis factor (TNF) family cytokine, receptoractivator of nuclear factor (NF)-κB ligand (RANKL), as well asmacrophage colony-stimulating factor (M-CSF) (30).

Recent studies have suggested that the nuclear factor of activatedT-cells (NFATc1) is a master switch for osteoclastogenesis in reponse toRANK receptor activation (31).

The necessary and sufficient role of NFATc1 in osteoclastogenesis wassuggested by the in vitro observation that NFATc1^(−/−) embryonic stemcells do not differentiate into osteoclasts (32).

The activation of NFAT c1 as well as of NFAT c2/c3/c4 is mediated by thecalcium/calmodulin dependant phosphatase, calcineurin A (CNA).

The inventors assessed the ability of some CNA-specific peptide aptamersto promote osteoclast differentiation via the activation of CNA. Raw1cells (osteoclasts precursors) were transfected with the followingplasmids: pCI-HA-Trx (negative control), pCI-HA CNA* (positive controlfor differentiation activation), pCI-HA R5G42, pCI-HA R5G42-C2, pCI-HAR5G42-C7, pCI-HA R5G42-C8 and pCI-HA R5G42-N9 (this last point mutantshows a dramatic reduction of the two hybrid interaction phenotypeagainst CNA compared to R5G42). The differentiation state was thenobserved 4 days post-transfection. As expected, cells in controlconditions (with RANKL) were differentiated into osteoclasts.

Some cells with the osteoclast phenotype can be observed with CNA*,R5G42, and R5G42-C7 (see FIG. 12), indicating that these proteins areable to initiate and fulfill the differentiation process. Neverthelesswith the negative control R5G42-N9 and the C2 and C8 mutants, some cellswith several nuclei can be observed but no osteoclasts fullydifferentiated were detectable in this experimental period.

Thus, the aptamers R5G42 and R5G42-C7 exert an effect on CNA sufficientto permit the differentiation of monocyte-derived cells into osteoclastsin the absence of RANKL.

Example 6 In Vivo Denervation Assay in Mice Tibia Muscles

Mice hind legs first received an injection of plasmids containingThioredoxin (TRX), a control aptamer (34) or only NaCl, followed byelectroporation. Their left hind legs were then denerved. Aftereuthanasia, total proteins were extracted, and the expression of certainkey proteins among which TRX, the aptamer 34 and its target (C34),Calcineurin A (CNA), beta-Tubuline (B-Tub), Bcl2 and Bax was checked.The level of CNA expression in muscle was high and TRX and the controlaptamer 34 cloned in the pCI-HA vector were detected (see FIG. 13).

Another group of mice hind legs were electroporated after the injectionof vectors containing TRX, the R5G42, C7 or N9 aptamers or with NaCl(control) at day 1. A unilateral abolition of the motor innervation ofthe tibia muscles of the left hind leg was performed at day 3 in orderto induce a muscular atrophy. The mice were then euthanised at day 17,i.e. 14 days after sciatic denervation of the left hind leg. The measureof the tibialis anterior area 14 days post-denervation showed thatwithout denervation (right hind leg), the muscle area is relativelystable from a one experiment to another (6.532.412+/−351.070, or 5.3% ofvariation). With denervation a reduced atrophy effect of about 27% and48% is observed with aptamers R5G42 and N9 as compared to the atrophyeffect obtained using the NaCl control (FIG. 18).

Example 7 Materials and Methods

The following section describes the materials and methods used in theabove-described examples.

Cell Culture

All mammalian cells were maintained in a 5% CO₂ atmosphere at 37° C. inDulbecco's Modified Eagle's Medium (Invitrogen-Gibco) supplemented with10% v/v fetal calf serum and 100 microg/ml penicillin-streptomycin.

Construction of Lentiviral Vectors

All the lentivectors were derived from pR4SA-EFS-GFP-W (19). This vectorfirst was digested with Hind III, thus eliminating EGFP, WPRE and EcoRIsites, to create pVRV1. The remaining EcoRI site upstream of the CMVpromoter was blunted and the vector was religated to create pVRV2. pVRV2was digested with BamHI and HindIII and the following hybridizedoligodeoxynucleotides:

(SEQ ID 1) 5′-GATCGCTAAGCGAATTCCTCGAGGCGCGCGTCGACCAGGATCC-3′ and(SEQ ID 2) 5′-AGCTTGGATCCTGGTCGACGCGCGCCTCGAGGAATTCGCTTAGC-3′

were ligated to create pVRV3, that bears a multiple cloning sequence.pVRV4 was constructed by inserting an IRES-EGFPf (famesylated enhancedGFP) coding sequence in pVRV3. This was done by a multiplex ligationbetween SalI/BamHI-cut pVRV3, a SalI/NcoI-cut EMCV IRES cassette (frompIRES2-EGFP, Clontech) and a NcoI/BamHI-cut EGFP-f coding sequence (frompEGFP-F, Takara Bio). A HA-tagged HTRX fragment from pJMX-HTRX (Abed etal, in preparation) was then PCR amplified using the oligonucleotides

5′-GCGGCTAAGCCATGTACCCTTATGATGTGCCAG-3′ (SEQ ID 3) and5′-GGAGACTTGACCAAACCTCTG-3′ (SEQ ID 4)

and this fragment was ligated into BlpI/XhoI-cut pVRV4. The resultingplasmid, pVRV6, directs the bicistronic expression of a HA-tagged humanTRX (with a modified active site) and of EGFP carrying a famesylationsequence so as to anchor the marker protein to plasma membranes.

Construction of the Peptide Aptamer Expression Library

pBK1, a library of peptide aptamers bearing 10 amino acids within theactive site of HA-tagged human TRX was constructed. The oligonucleotides

(SEQ ID 5) 5′-TGGGCCGAGTGGAGCGGTCCG(NNS)₉NNCGGACCGAGCAAGATGATCGCCCC-3′

where N is A, C, G or T and S is C or G, and

5′-GGGGCGATCATCTTGCTCGGTCCG-3′ (SEQ ID 6)

were annealed and duplexes were produced using the Klenow DNApolymerase. The AvalI-cut duplexes were ligated into CpoI-cut pVRV6. Theligation product was transformed into ElectroTen Blue competent bacteria(Stratagene) and 8.5×10⁹ transformants were obtained.

Viral Vector Production

Lentiviral particles were produced by transfecting into 293T cells thefollowing plasmids: i) pVRV6, pVRV12 (pVRV6 directing the expression ofp21^(Cip1)), pBK1 or any aptamer sub-library; ii) helper pSIV15,directing the expression of gag and pol (20); iii) FbmoSalf, directingthe expression of a murine ecotropic envelope (19); iv) pRev (20). Insome experiments, plasmids iii and iv were replaced by the G-rev plasmid(20), directing the expression of Rev and the VSV-G pantropic envelope.Lentivirus-containing supernatants were collected and filtered 48 hpost-transfection through a 0.45 micron filter. Viral titers weredetermined by infecting XC or Hela cells and counting GFP-positive cellswith a cytometer (FACScan, Becton-Dickinson). From 40% to 100% cellswere routinely infected.

Screening of Antiproliferative Peptide Aptamers

XC cells were plated 24 h before infection (2×10⁵ cells/well, 6-wellplates, 6 plates). To infect the cells, a medium containing a viralsupernatant and 6 microg/ml polybrene was added. Three days later, thecells were collected, washed with PBS, stained 5×10⁵ cells/ml with 10microM CellTracker™ Orange CMTMR (Invitrogen) in PBS at 37° C. for 30min and incubated in culture medium for another 30 min at 37° C. Thecells were then plated onto 10 cm dishes (10⁶ cells/dish). After 72 h,the cells were collected and the highest percentile of CMTMR fluorescentcells was sorted using a FACS Vantage flow cytometer (Becton-Dickinson).The sorted cells were pooled and their genomic DNA was extracted using aWizard Genomic DNA purification kit (Promega). Aptamer coding genes werePCR amplified using the oligonucleotides

5′-AACCGGTGCCTAGAGAAGGT-3′ (SEQ ID 7) and 5′-AGACCCCTAGGAATGCTCGT-3′.(SEQ ID 8)

The EcoRI/XhoI-digested products were cloned into EcoRI/XhoI-cut pVRV6,to create successive sub-libraries of peptide aptamers, named pCMTMR 1to 7.

Two-Hybrid Screening of R5G42-Interacting Proteins

pVRV6-R5G42 was digested with EcoRI and XhoI and ligated the fragmentinto EcoRI/XhoI-cut pGILDA (Clontech) to create pGILDA-R5G42, a plasmiddirecting the galactose-inducible expression of a LexA-R5G42 fusionprotein. MB226α pSH18-34 yeast (21) was transformed with pGILDA-R5G42and MB210a yeast (21) with human foetal brain and human testes cDNAlibraries, constructed in pJG4-5. The yeast-two hybrid screening of bothlibraries was performed essentially as described (21), using 4×10⁸ cfuand 2.4×10⁸ cfu from the brain and testes libraries, respectively. Themating efficiency was estimated at 50% and 58% and the number of diploidexconjugants at 0.2×10⁸ and 1×10⁸ for the brain and testis cDNA librarytransformed yeast, respectively. The expression of the bait and thelibraries were induced at 30° C. for 5 h, from 10% of the diploids. Theyeast were collected and plated onto 10 Ura⁻His⁻Trp⁻Leu⁻galactose/raffinose plates for 5 days, then replica plated onto 10Ura⁻His⁻Trp⁻Ade⁻ X-gal galactose/raffinose plates. 60 clones were pickedfrom the brain and 48 clones from the testes library that grew inabsence of leucine and adenine, and that displayed a β-galactosidaseactivity. Library plasmids were recovered and re-transformed intoEGY48α. The interaction phenotypes were confirmed by a mating assay withEGY42a transformed with pGILDA-R5G42. The library cDNAs were thensequenced from most reconfirmed clones.

Yeast Two-Hybrid Mating Assays

To build the different truncations of the CNAβ Cter interacting clone,oligonucleotides that enabled cloning the PCR products into pJG4-5 byhomologous recombination were designed.

RH6: (SEQ ID 9) 5′-TTATGATGTGCCAGATTATGCCTCTCCCGAATTCagtatttgctctgatgatg-3′ RH4: (SEQ ID 10)5′-AAACCTCTGGCGAAGAAGTCCAAAGCTTCTCGAGCTActgtacag catattccg-3′ RH3:(SEQ ID 11) 5′-AAACCTCTGGCGAAGAAGTCCAAAGCTTCTCGAGCTAggcactttgcagggtctgc-3′ RH7: (SEQ ID 12)5′-ACCTCTGGCGAAGAAGTCCAAAGCTTCTCGAGTCAcctgagaaca gagaagact-3′

The 5′ end of RH6 (upper case) matches part of the HA epitope tag andthe 5′ ends of RH4, RH3 and RH7 (upper case) match the 5′ extremity ofthe ADH terminator. The PCR reactions was performed usingpCMV-SPORT6-CnAβ as a template. CnAβCter Δ1, Δ2, CaM were constructed bycombining oligonucleotides RH6/RH4, RH6/RH3, RH6/RH7, respectively.MB210a was co-transformed with the PCR products and EcoRI/XhoI-cutpJG4-5. The prey plasmids were retrieved from the transformants (21) andthe homologous recombination products were checked by sequencing. MB210awas also transformed with positive and negative controls of interaction.TB50α was co-transformed with pSH18-34T (a plasmid bearing ahigh-sensitivity lacZ reporter gene) and pGILDA directing the expressionof LexA, LexA-R5G42, LexA-R7G44 and LexA-R5G52. The yeast two-hybridmating assays were performed as described (21).

In Vitro Binding Assay

pVRV6-aptamer plasmids were first digested with EcoRI and XhoI and thefragments were ligated into EcoRI/XhoI-cut pGEX4T1. GST-aptamer fusionswere expressed in a BL-21(DE3) E. coli strain. Overnight cultures werediluted 1/100 and let to grow at 37° C. to reach an OD₆₀₀ of 0.6 to 0.8.The expression of fusion proteins was induced by adding 1 mM IPTG andincubating overnight at 20° C. with vigorous shaking. The bacteria werecollected and resuspended into a lysis buffer (50 mM Tris pH8, 100 mMNaCl, 1 mM DTT) containing 1 mg/ml lysozyme. They were frozen and thawedthree times and sonicated on ice. The lysates were centrifuged at 13000g for 30 min and the soluble fractions were collected. Equal amounts ofGST-aptamers were immobilized on 100 μl glutathion sepharose 4B beads(Amersham) at room temperature for 20 min. The beads were washed threetimes with lysis buffer. The beads were incubated with 1 or 3 μg ofbovine brain purified calcineurin (Upstate) for 1 h at 4° C. The beadswere then washed five times with lysis buffer and the bound protein waseluted by boiling samples 10 min in presence of electrophoresis loadingbuffer. The samples were loaded onto a SDS-PAGE, transferred tonitrocellulose membrane, and calcineurin was detected bywestern-blotting using an anti-calcineurin pan A antibody (1/1000,Chemicon International). The blot was revealed using a HRP-linked rabbitantiserum and an ECL kit (Perkin Elmer).

Cell Proliferation Assay

To stably express peptide aptamers in mammalian cells, the episomaleukaryotic expression vector pCEP4 that bears a CMV promoter and ahygromycin selection marker (InVitrogen) was used. Aptamer codingsequences were PCR amplified using the oligonucleotides

5′-GCAAGCTAGCATGTACCCTTATGATGTGCCA-3′ (SEQ ID 13)

that hybridized to the HA coding sequence and

5′-CGTTGCGGCCGCTTAGACTAATTCATTAATGGT-3′ (SEQ ID 14)

that contained a stop codon. The PCR products were digested with NheIand NotI and ligated into NheI/NotI-cut pCEP4 to create pEA-aptamerplasmids. 3×10⁵ cells/well were plated in 6-well plates and transfected24 h after using Jet PEI (Qbiogen), 3.7 μg pEA-aptamer plasmids and 0.3μg pEGFP-C1 (Clontech) to monitor transfection. Hygromycin (InVitrogen)was added at 200 μg/ml two days later and the cells were cultured for 2weeks, renewing the medium twice a week. The cells were then rinsed inPBS and were fixed and stained by incubating 30 min in crystal violet(0.05% crystal violet, 20% ethanol, 0.37% formaldehyde). Excess crystalviolet was removed by washing with water.

In Vitro Phosphatase Assay

GST-aptamer fusion proteins were first produced as described above. Forthis experiment, GST-aptamer fusion proteins were eluted from glutathionsepharose beads using 20 mM reduced L-glutathione (Sigma), and theeluates were dialyzed overnight against a phosphatase buffer (50 mMTris-HCl pH7.4, 0.1 mM CaCl₂). The phosphatase activity of calcineurinwas measured using pNPP (Sigma) as substrate, in a final volume of 100μl. The sample solution contained 50 mM Tris-HCl (pH7.4), 0.1 mM CaCl₂,1 mM NiSO₄, 0.15 mg/ml BSA (Sigma), 0.1 μM calcineurin (Upstate).Purified calmodulin (Upstate) and GST-aptamer fusion proteins were addedat different concentrations (see figure legend). After a 15 minpre-incubation at 37° C., the reactions were started by adding 4.1 mMpNPP and the mixtures were incubated at 37° C. for 20 min. Thenitrophenylate product was measured at 405 nm using an Envision platereader (Perkin Elmer). The background level that was determined wassubstracted using a mixture lacking calcineurin.

Monitoring of Bad Phosphorylation

The peptide aptamer coding genes were cloned into pPEAt (a pCEP4-basedvector that bears a tetracyclin-inducible promoter and a hygromycinresistance gene), as described above (”cell proliferation assay“).

4×105 Hela-tet cells/well were seeded in a 6-well plate 24 h beforetransfection. 1 μg of pEBG-mBad (a plasmid directing the expression ofthe murine Bad protein; Cell Signaling Technology), 0.5 μg ofpCMV-SPORT6-CnAβ and pCMV-SPORT6-CnB (plasmids directing the expressionof human calcineurin Aβ and B; RZPD), and 1 μg of pPEAt-R5G42, -R5G52 or-R7G44 were transfected with Jet PEI (Qbiogen). After an overnightincubation of the transfection mix, the cells were washed once withculture medium and fresh medium was added, with or without 0.5 μM FK506(Calbiochem). The cells were collected 24 h later, washed twice in PBS,and lysed 20 min in ice-cold lysis buffer (20 mM Tris, pH 7.4, 150 mMNaCl, 2 mM EDTA, 1% NP40, protease inhibitor cocktail complete EDTAfree-Roche). The lysates were centrifuged to remove cellular debris andthe protein content was quantified using the microBCA protein assay kit(Pierce). 50 μg of the lysates were loaded on a 4-12% SDS-PAGE,transferred to nitrocellulose membranes, and blotted withanti-phospho-Bad (Ser112), anti-phospho-Bad (Ser136), and anti-Badantibodies (Cell Signaling Technology). The blots were revealed usingthe enhanced chemiluminescence (ECL) system (Perkin Elmer).

Raw Cell Differentiation Assay.

Raw1 cells were transfected with the following plasmids: pCI-HA-Trx(negative control), pCI-HA CNA* (positive control for differentiationactivation), pCI-HA R5G42, pCI-HA R5G42-C2, pCI-HA R5G42-C7, pCI-HAR5G42-C8 and pCI-HA R5G42-N9. The sequence of CNA* is the same as thatof CNA8 (see FIG. 17, SEQ ID 42). The sequences of the R5G42 (SEQ ID22), C2 (SEQ ID 23), C7 (SEQ ID 27), C8 (SEQ ID 28) and N9 (SEQ ID 33)aptamers is shown on FIG. 8.

One day before the transfection, Raw I cells were plated in 6-welldishes at 50 cell/mm². Transfection was performed with FuGene 6 Reagent(Roche) using 2 μg of each plasmid and following supplierrecommandations.

8 h after transfection D-MEM was changed with α-MEM. In the controldishes α-MEM+50 ng/ml RANKL was added. After 2 days, medium was changedwith a fresh medium. The differentiation state was then observed 4 dayspost-transfection.

Vectors for Yeast Two-Hybrid, Mammalian Cells and In Vivo Assays

The vectors used in the series of experiments are listed in table 3.

The amplification is performed first starting from several isolatedbacteria colonies, in 5 ml culture media which allows to obtain a smallamount of DNA (Miniprep), sufficient to determine if the cloning wasefficient. The genes are then sequenced in order to eliminate errorswhich could have occurred during the PCR process. If the plasmids are tobe used to transfect human or animal cells, a larger quantity is thenproduced from 300 ml of culture (Maxiprep)

CNA fragments were cloned in HA-pJG4-5 vectors for the yeast two-hybridanalysis preys. The aptamers and mutants of R5G42 were cloned in pCI-HAvectors for the expression in mammalian cells and in pBof (cGFP; doublepromoter) for expression in animals. pGEX vectors were also prepared forexpression of the aptamers in bacteria. The sequences of all vectorswere checked.

In Vivo Tibia Muscles Denervation Assay in Mice (Length: 17 Days)

Day 1

General Anaesthesia of the Mice

Four weeks old animals were anaesthetised with a mix of ketamine 50(PANPHARMA, Ref: PF250211) and Xylazine hydrochloride (Sigma Ref X1251)(2/3, 1/3). Intra-peritoneal injections were performed (120 μl for a 25g mouse, adjusted in function of the weight).

Injection of the Plasmids in the Ie Tibialis

Mice hind legs were shaved. Both hind legs received an intra-muscularinjection with vectors containing TRX, the R5G42, C7 or N9 aptamers, acontrol aptamer (34) or NaCl (control) in order to obtain anover-expression of a gene in the muscle. The plasmid DNA (purified bycesium chloride) was diluted in NaCl 4.5% filtered 0.22 μm. Afterdisinfection with ethanol 70% of the anterior surface of the tibia, 30μl containing 5 μg of plasmid DNA containing the aptamer and 2 μg ofplasmid DNA containing a nuclear GFP were injected trans-cutaneously.

Electroporation

An electric field was applied to the muscle to allow the entry of theplasmid DNA into the muscular fibres.

A thin layer of echography gel was applied on both sides of the tibia.The electric field applied corresponded to eight 20 millisecondsimpulses spaced by 500 milliseconds, at 200 Volts/cm.

Day 3

Sciatic Denervation

The mouse was positioned on its right flank. The left hind leg and theflank were disinfected. A cutaneous incision was performed in thesuperior third of the thigh. The conjunctive sheath was cut withoutharming the two muscular masses beneath. The sciatic nerve can be foundbetween the two masses on passing a forceps in the middle. It wassectioned at two spots at 5 mm from each other, starting from theafferent side. The skin was then sutured.

Day 17

Euthanasia of the Animals

The mice were euthanised by cervical dislocation after generalanaesthesia.

The anterior tibialis were removed and fixed on a cork lid with a gumand rapid freezing was performed by diving the whole in liquid nitrogenchilled methycyclohexane. The muscles were thus conserved at −80° C.

Treatment of the Samples

Cryosections

10 μm sections were prepared with a cryostat and placed on slides. Theslides were conserved at −80° C.

Immunostaining

The selected slides were treated with the MOM Kit (Vector laboratories,PK-2200).

The sections allow to highlight the slow fibres (MyHC slow antibodies,Sigma, M8421) and the rapid fibres (MyHC Fast, Sigma, M4276).

The developments were performed with DAB (SK-4100) and VIP kits fromVector Laboratories.

The baths were photographed with a binocular magnifier (Binoluminar), at0.8× optic, and 20× digital enlarging.

The analysis of the surfaces of the muscles was performed with theMetamorph software (version 6).

Tables

TABLE 1 Occurrence of antiproliferative peptide aptamers after the lastscreening iteration and variable region sequences. Amino acids in lowercase correspond to the HTRX flanking residues. Peptide Occurrence inSequence of Aptamer 7^(th) sub-library variable region R5G42 0.41 . . .cgpSAVTFAVCALgpc . . . R7G11 0.09 . . . cgpLHLAGRGWENgpc . . . R5G520.08 . . . cgpIQSPPESPTGgpc . . . R7G44 0.014 . . . cgpHQSTIGVAEFgpc . ..

TABLE 2 Results of the yeast two-hybrid screening against R5G42. Thetable lists the different clones selected from the brain and testeslibraries and sequenced. Bold numbers correspond to strong, specifictwo-hybrid interaction phenotypes. Plain numbers correspond to weak,specific interaction phenotypes. Numbers in italics correspond tonon-specific clones, which show two-hybrid interaction phenotypes withother peptide aptamers. Testes Accession Brain library library NumberCNAβ 1 NP_066955 CNAγ 2 NP_005596 NS5ATP2 29  9 NP_057147 Proteasome β 5subunit 1 NP_002788 Maspardin 3 NP_057714 K channel 5 NP_076419tetramer. domain Hypothetical protein 1 XP_943453.1 Adaptor protein withPH 1 NP_066189.1 and SH2 domains Sorting nexin 9 1 NP_057308 CDC42(GEF9) 5 NP_056000 Promyelocytic leukemia 2 NP_005997 Zn finger proteinFascin 3 1 NP_065102.1

TABLE 3 Plasmids Yeast two- Expression Bacterial hybrid

Expression pJG4-5, pGilda, pEG202 Cells Empty pGex-4T1 pGilda pJG4-5pCI-HA plasmids GST Fusion Bait Prey HA Tag Aptamers Mini Maxi Seq MiniMaxi Seq Mini Max Seq Mini Maxi Seq R5G42 + + + + + + + + + + + +R5G42-C2 + + + + + + R5G42-C7 + + + + + + + + + R5G42-C8 + + + + + +R5G42-N9 + + + + + + R5G52 + + + + + + + + + R5G44 + + + + + + + + +HTrx + + + + + + + + + Expression Expression Production of

recombinant Cells pBCF lentivirus pCI-HA pEAt

pGREV, pEA Inducible HA Tag and pRev, SIV15, Empty Inducible expressioneGFP co- pVRV6 plasmids expression and Tag expression pVRV6 AptamersMini Maxi Seq Mini Maxi Seq Mini Maxi Seq Mini Maxi SeqR5G42 + + + + + + + + + + + + R5G42-C2 + + + + + + + + +R5G42-C7 + + + + + + + + + R5G42-C8 + + + + + + R5G42-N9 + + + + + +R5G52 + + + + + + + + + + + + R5G44 + + + + + + + + + + + +HTrx + + + + + + + + + + + + pEG202 pJG4-5 pCI-HA pET15b Bait Prey pCMVpSPORT HA Tag Calcineurin Mini Maxi Seq Mini Maxi Seq Mini Max Seq MiniMaxi Seq Mini Maxi Seq Mini Maxi Seq CNA1 (WT) + + + + nn + + + + + + +CNA2 + nn + CNA3 + nn + CNA4 + nn + CNA5 + nn + CNA6 + nn + CNA7 + nn +CNA8 + nn + + + + CNA9 + nn + CNA10 + nn + CNA11 + nn + CNAγ + + + + + +pJG4-5 pET15b Prey NS5A-TP2 Mini Maxi Seq Mini Maxi Seq Mini Max SeqNS5A-TP2 + + + + + + +: Construction performed in laboratoire nn: notnecessary mini: Miniprep maxi: Maxiprep Seq: Sequencing

indicates data missing or illegible when filed

REFERENCES

1. Herskowitz, I. (1987) Functional inactivation of genes by dominantnegative mutations. Nature 329, 219-222

2. Richardson, J. H. and Marasco, W. A. (1995) Intracellular antibodies:development and therapeutic potential. Trends Biotechnol. 13, 306-310

3. Rimmele, M. (2003) Nucleic acid aptamers as tools and drugs: recentdevelopments. Chembiochem. 4, 963-971

4. Hoppe-Seyler, F., Cmkovic-Mertens, I., Tomai, E. and Butz, K. (2004)Peptide aptamers: specific inhibitors of protein function. Curr. Mol.Med. 4, 529-538

5. Silva, J., Chang, K., Hannon, G. J. and Rivas, F. V. (2004)RNA-interference-based functional genomics in mammalian cells: reversegenetics coming of age. Oncogene 23, 8401-8409

6. Strausberg, R. L. and Schreiber, S. L. (2003) From knowing tocontrolling: a path from genomics to drugs using small molecule probes.Science 300, 294-295

7. Deiss, L. P. and Kimchi, A. (1991) A genetic tool used to identifythioredoxin as a mediator of a growth inhibitory signal. Science 252,117-220

8. Gudkov, A. V., Kazarov, A. R., Thimmapaya, R., Axenovich, S. A.,Mazo, I. A. and Roninson, I. B. (1994) Cloning mammalian genes byexpression selection of genetic suppressor elements: association ofkinesin with drug resistance and cell immortalization. Proc. Natl. Acad.Sci. U.S.A. 91, 3744-3748

9. Li, Q. X., Robbins, J. M., Welch, P. J., Wong-Staal, F. and Barber,J. R. (2000) A novel functional genomics approach identifies mTERT as asuppressor of fibroblast transformation. Nucleic Acids Res. 28,2605-2612

10. Xu, X., Leo, C., Jang, Y., Chan, E., Padilla, D., Huang, B. C., Lin,T., Gururaja, T., Hitoshi, Y., Lorens, J. B. et al. (2001) Dominanteffector genetics in mammalian cells. Nat. Genet. 27, 23-29

11. Paddison, P. J., Silva, J. M., Conklin, D. S., Schlabach, M., Li,M., Aruleba, S., Balija, V., O'Shaughnessy, A., Gnoj, L., Scobie, K. etal. (2004) A resource for large-scale RNA-interference-based screens inmammals. Nature 428, 427-431

12. Pestov, D. G. and Lau, L. F. (1994) Genetic selection ofgrowth-inhibitory sequences in mammalian cells. Proc. Natl. Acad. Sci.U.S.A. 91, 12549-12553

13. Hitoshi, Y., Gururaja, T., Pearsall, D. M., Lang, W., Sharma, P.,Huang, B., Catalano, S. M., McLaughlin, J., Pali, E., Peelle, B. et al.(2003) Cellular localization and antiproliferative effect of peptidesdiscovered from a functional screen of a retrovirally delivered randompeptide library. Chem. Biol. 10, 975-987

14. Colas, P., Cohen, B., Jessen, T., Grishina, I., McCoy, J. and Brent,R. (1996) Genetic selection of peptide aptamers that recognize andinhibit cyclin-dependent kinase 2. Nature 380, 548-550

15. Xu, C. W., Mendelsohn, A. R. and Brent, R. (1997) Cells thatregister logical relationships among proteins. Proc. Natl. Acad. Sci.U.S.A. 94, 12473-12478

16. Geyer, C. R., Colman-Lemer, A. and Brent, R. (1999) “Mutagenesis” bypeptide aptamers identifies genetic network members and pathwayconnections. Proc. Natl. Acad. Sci. U.S.A. 96, 8567-8572

17. Norman, T. C., Smith, D. L., Sorger, P. K., Drees, B. L., O'Rourke,S. M., Hughes, T. R., Roberts, C. J., Friend, S. H., Fields, S. andMurray, A. W. (1999) Genetic selection of peptide inhibitors ofbiological pathways. Science 285, 591-595

18. Blum, J. H., Dove, S. L., Hochschild, A. and Mekalanos, J. J. (2000)Isolation of peptide aptamers that inhibit intracellular processes.Proc. Natl. Acad. Sci. U.S.A. 97, 2241-2246

19. Mangeot, P. E., Duperrier, K., Negre, D., Boson, B., Rigal, D.,Cosset, F. L. and Darlix, J. L. (2002) High levels of transduction ofhuman dendritic cells with optimized SIV vectors. Mol. Ther. 5, 283-290

20. Negre, D., Mangeot, P. E., Duisit, G., Blanchard, S., Vidalain, P.O., Leissner, P., Winter, A. J., Rabourdin-Combe, C., Mehtali, M.,Moullier, P. et al. (2000) Characterization of novel safe lentiviralvectors derived from simian immunodeficiency virus (SIVmac251) thatefficiently transduce mature human dendritic cells. Gene Ther. 7,1613-1623

21. Bickle, M., Dusserre, E., Moncorgé, O., Boffin, H. and Colas, P.(2006) Selection and characterization of large collections of peptideaptamers through optimized yeast two-hybrid procedures. Nat. Protoc. inpress

22. Yang, Q., Cheng, J., Liu, Y., Hong, Y., Wang, J. J. and Zhang, S. L.(2004) Cloning and identification of NS5ATP2 gene and its splicedvariant transactivated by hepatitis C virus non-structural protein 5A.World J. Gastroenterol. 10, 1735-1739

23. Aramburu, J., Heitman, J. and Crabtree, G. R. (2004) Calcineurin: acentral controller of signalling in eukaryotes. EMBO Rep. 5, 343-348

24. Kahl, C. R. and Means, A. R. (2003) Regulation of cell cycleprogression by calcium/calmodulin-dependent pathways. Endocr. Rev. 24,719-736

25. Wang, H. G., Pathan, N., Ethell, I. M., Krajewski, S., Yamaguchi,Y., Shibasaki, F., McKeon, F., Bobo, T., Franke, T. F. and Reed, J. C.(1999) Ca2+-induced apoptosis through calcineurin dephosphorylation ofBAD. Science 284, 339-343

26. Ke, H. and Huai, Q. (2003) Structures of calcineurin and itscomplexes with immunophilins-immunosuppressants. Biochem. Biophys. Res.Commun. 311, 1095-1102

27. Baines, I. C. and Colas, P. (2006) Peptide aptamers as guides forsmall molecule drug discovery. Drug Disc. Today, 11, 334-341

28. Gururaja, T., Li, W., Catalano, S., Bogenberger, J., Zheng, J.,Keller, B., Vialard, J., Janicot, M., Li, L., Hitoshi, Y. et al. (2003)Cellular interacting proteins of functional screen-derivedantiproliferative and cytotoxic peptides discovered using shotgunpeptide sequencing. Chem. Biol. 10, 927-937

29. Hogan P. G., Chen L., Nardone J. and Rao A. (2003) Transcriptionalregulation by calcium,calcineurin, and NFAT. Genes and Dev. 17,2205-2232

30. Asagiri M, Takayanagi H. The molecular understanding of osteoclastdifferentiation. Bone 40 (2006) 251-264

31. Zhu L L, et al . RANK-L induced the expression of NFATc1, but not ofNFkB subunits durino osteoclast formation. Biochemical and BiophysicalResearch Communications 326(2005) 131-135

32. Takayanagi H et al,.lnduction and activation of the transcriptionfactor NFATc1 integrate RANKL signaling for terminal differentiation ofosteoclasts. Dev Cell 3 (2002) 889-901

1. A polypeptide comprising or consisting essentially of: (i) the aminoacid sequence SAVTFAVCAL (SEQ ID 20), or (ii) the amino acid sequenceGPSAVTFAVCALGP (SEQ ID 21), or (iii) a variant of the amino acidsequence (i) or (ii) having one amino acid change, said polypeptidebeing capable of binding to a protein which comprises at least thesequence extending from amino acid 378 to 500 of the beta isoform ofcalcineurin A, to Calcineurin A or to NS5A-TP2.
 2. (canceled)
 3. Apolypeptide according to claim 1, having a modulatory effect on a cell,wherein said cell is a eukaryotic cell, a mammalian cell, an animalcell, a murine cell or a human cell.
 4. A polypeptide according to claim3, wherein said cell is a muscle, bone, neuronal or cardiac cell.
 5. Apolypeptide according to claim 3, to wherein said polypeptide has anantiproliferative or differentiating effect on said cell.
 6. Apolypeptide according to claim 3, wherein said polypeptide activatesNFAT.
 7. A polypeptide according to claim 1, wherein said amino acidsequence (i), (ii) or (iii) is conformationally constrained bycovalently binding to a scaffold molecule.
 8. A polypeptide according toclaim 7, wherein said amino acid sequence (i), (ii) or (iii) is bound tothe scaffold at both C and N termini.
 9. A polypeptide according toclaim 8, wherein said amino acid sequence (i), (ii) or (iii) is locatedbetween two cysteines.
 10. A polypeptide according to claim 7, whereinthe scaffold molecule is a thioredoxin, a thioredoxin-like protein, anuclease, a protease, a protease inhibitor, an antibody or astructurally-rigid fragment of an antibody, a fluorescent protein, or aconotoxin.
 11. A polypeptide according to claim 10, wherein the scaffoldmolecule is human thioredoxin and said amino acid sequence (i), (ii) or(iii) is located between the two cysteines located at positions 32 and35.
 12. A polypeptide according to claim 1, which binds to calcineurinthrough said amino acid sequence (i), (ii) or (iii).
 13. A polypeptideaccording to claim 1, which binds to the calcineurin A subunit.
 14. Apolypeptide according to claim 13 which binds to at least one of thealpha, beta or gamma isoforms of human calcineurin A (CNA).
 15. Apolypeptide according to claim 13 which binds to CNA at a site locatedwithin the sequence extending from the amino terminal of the calmodulinbinding domain to the carboxy terminal of the auto-inhibitory domain ofCNA, wherein said site is not limited to the calmodulin binding domain.16. A polypeptide according to claim 14 which binds to the human CNAbeta isoform at a site located within the sequence extending from aminoacid 378 to
 500. 17. A fusion protein comprising the polypeptide ofclaim 1 covalently bound at its amino or carboxy terminus to anotherprotein.
 18. A nucleic acid sequence comprising or consistingessentially of a sequence encoding the polypeptide of claim
 1. 19. Avector comprising the nucleic acid sequence of claim
 18. 20. Aeukaryotic cell comprising the polypeptide of claim 1, a nucleic acidsequence encoding such polypeptide or a vector comprising such nucleicacid sequence.
 21. A eukaryotic cell according to claim 20, wherein saideukaryotic cell is a mammalian cell.
 22. (canceled)
 23. A method fortreating or preventing in a subject in need thereof a condition whichcan be treated or prevented by upregulating the intracellularphosphatase activity of calcineurin in eukaryotic cells or by activatingNFAT which comprises administering to the subject the polypeptide ofclaim 1, a nucleic acid encoding such polypeptide or a vector comprisingsuch nucleic acid.
 24. A method for treating or preventing in a subjectin need thereof a condition which can be treated or prevented bylimiting the proliferation or inducing the differentiation of eukaryoticcells which comprises administering to the subject the polypeptide ofclaim 1, a nucleic acid encoding such polypeptide or a vector comprisingsuch nucleic acid.
 25. The method according to claim 23, wherein saideukaryotic cells are cancer cells, cardiomyocytes, neurones,fibroblasts, myocytes, satellite cells, skeletal muscle cells,osteoblasts, osteoclasts, or T-cells.
 26. The method according to claim23, wherein said eukaryotic cells are mammalian cells.
 27. The methodaccording to claim 23, wherein said condition is associated with NFATphosphorylation state, T-cell activation state, skeletal myocytedifferentiation stage, skeletal muscle dystrophy or atrophy, neuronedevelopment, bone formation or osteoclast differentiation.
 28. Themethod according to claim 23, wherein said condition is Duchennemuscular dystrophy, osteopetrosis, cancer or a farcted area in theheart.
 29. A method for the identification of substances which modulatethe interaction between CNA and the polypeptide of claim 1 comprisingthe steps of: (i) contacting a candidate modulatory substance with CNAand the polypeptide conditions in which CNA and said polypeptide canbind, and in which said binding can be detected by a specific signal;(ii) detecting a change in the intensity of said signal; and (iii)optionally recovering the candidate substance.
 30. A method forintracellular identification of substances which modulate theinteraction between CNA and the polypeptide of claim 1 comprising thesteps of: (i) introducing a candidate substance, CNA and the polypeptideinto a eukaryotic cell, in conditions in which a specific detectablephenotype associated to the binding of CNA with the polypeptide can bedetected; (ii) detecting a change of the said specific detectablephenotype; and (iii) optionally recovering the candidate substance.31-32. (canceled)
 33. The method according to claim 30, where saidspecific detectable phenotype consists in the expression of a reportergene, a modification of the proliferative rate of the cells, cellapoptosis, a modification of cell differentiation or resistance to celldeath.
 34. The method according to claim 30, where said conditionscomprise the use of a two-hybrid assay.
 35. A method for modulatingcalcineurin activity in vivo or in vitro comprising contactingcalcineurin with a ligand capable of binding to calcineurin at a sitelocated within the sequence extending from the amino terminal of thecalmodulin binding domain to the carboxy terminal of the auto-inhibitorydomain of CNA, said site not being limited to the calmodulin bindingdomain in conditions suitable to allow effective binding between theligand and calcineurin thereby modulating at least one activity ofcalcineurin. 36-37. (canceled)
 38. The method according to claim 35,where said activity is a phosphatase activity.
 39. A polypeptideaccording to claim 1, wherein said polypeptide has an differentiatingeffect on osteoclasts in the absence of RANKL.
 40. A method forenhancing transcription of a gene in a cell, said gene being under thetranscriptional control of a regulatory element, particularly apromoter, containing at least one NFAT-response element, which comprisesintroducing a polypeptide according to claim 1 into said cell.
 41. Apolypeptide according to claim 10, wherein the scaffold molecule isRNaseA, trypsin, eglin C, GFP, YFP, human thioredoxin, or E. colithioredoxin A.
 42. The method according to claim 26, wherein saidmammalian cells are human cells.